data wrangling for
computational genomics
 

basespace-download

basespace-download is a tool for downloading FASTQ files from Illumina’s BaseSpace cloud service. For some instruments, analysis happens (by default) in the cloud, which can make retrieval difficult. Thankfully, Illumina provides a good API for interacting with BaseSpace. This tool makes downloading files for a particular sample or project very simple.

App-token

You must possess a valid app-token from BaseSpace in order to use this application. This is your method for authenticating with BaseSpace.

For more information on getting an app-token, see here: https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader

Usage

USAGE:
   basespace-download [arguments...]

ARGUMENTS:
   -t           Application token from BaseSpace [$BASESPACE_APP_TOKEN]
   -s           Sample ID to download
   -p           Project ID to download (all samples)
   --dr         Dry-run (don't download files)
   --help, -h       show help
   --version, -v    print the version

Building from scratch

You need to have Go installed first. Next, you can retrieve the Go code and build it in one step:

go get github.com/compgen-io/basespace-download

Next, you can copy the binary from $GOPATH/bin to anywhere in your $PATH.